[Bioperl-l] BL2SEQ

[Mane, Ajay (UMR-Student)]

Thanks for the reply.
 
I have lots of sequence pairs which i want to align. Two sequences at a time. I want to form some statistics on the alignment results. That is about the coding regions in nucleotides. I need to manually look at the coding regions everytime and do some analysis. Instead, i want to run a perl file which runs the bl2seq on blast server, gets the results, formats them to provide some statistics which i am interested in. I do not want to install blast locally on my machine. I just have lots of accession numbers in a file and want to display statistics of all of them in some file/files using a perl file. I have succeeded to a limit using the normal perl, by submitting accession numbers and getting results from blast server using http::request methods. But i want to know how to use Bioperl for this job.
 
Thanks,
Ajay

 
________________________________

From: Barry Moore [mailto:barry.moore at genetics.utah.edu]
Sent: Wed 3/30/2005 2:48 PM
To: Mane, Ajay (UMR-Student)
Subject: Re: [Bioperl-l] BL2SEQ



Ajay-

Not sure what you want to do with your blast results, but I think you'd
be pretty limited in doing much analysis using bioperl from the perl
command line.  You might look at the SEALS package
http://www.ncbi.nlm.nih.gov/CBBresearch/Walker/SEALS/, or repost with
more detail about what it is that you are trying to do.

Barry

Mane, Ajay (UMR-Student) wrote:

>I have mailed earlier to this group, but there was no response. I want to run perl from a command line to get the
>results of NCBI bl2seq tool, which aligns two sequences. Which are the modules to be used ? A reply atleast this time
>would be great.
>
>- Ajay
>
>________________________________
>
>From: bioperl-l-bounces at portal.open-bio.org on behalf of Madeleine Lemieux
>Sent: Wed 3/30/2005 11:26 AM
>To: bioperl-l at portal.open-bio.org
>Subject: [Bioperl-l] BLASTP
>
>
>
>Minyi,
>
>Are you sure both versions of Blast are getting the same e-val? The
>RemoteBlast.pm default is 1e-3 but Perl.pm sets it at 1e-10. I'm not
>sure what the standalone value is.
>
>-Madeleine
>
>_______________________________________________
>Bioperl-l mailing list
>Bioperl-l at portal.open-bio.org
>http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
>
>_______________________________________________
>Bioperl-l mailing list
>Bioperl-l at portal.open-bio.org
>http://portal.open-bio.org/mailman/listinfo/bioperl-l
> 
>

--
Barry Moore
Dept. of Human Genetics
University of Utah
Salt Lake City, UT